Phylogenetic analysis of HIV-1 env -V3 sequences. NJ tree of HIV-1 env-V3 nucleotide fragments obtained from blood and seminal plasma collected in 2001–2005. Distances were calculated with the Tamura-Nei method using the gamma model with α = 0.38, and 1000 bootstrap replicated were analysed. The three separate clusters comprised of strains B1, B2, and CRF01_AE are indicated. A representative sequence set was used to generate the phylogenetic tree.